web1 user cant login to desktop anymore

I have a client that was "hakked by da JAKAL", damage appeared to be minimal and was repaired by dumping the contents of my web1 home folder ((/srv/www/web1/web/)except for stats and errors folders)) and doing a restore of my site that I had backed up earlier that day. The thing is 1. I unpacked the backup while logged in as root and the folder privileges were all wrong. When trying to change them I can change the values but still can't write to them as the web1 user. 2. I can no longer login to the desktop as the web1 user. When I try, I get the message "Xsession: Login for web1 user is disabled" but is not when I look in the yast user config. My site is online and functioning.

I also noticed that in the user administration utility under groups, all my ispconfig sites and admispconfig (uid 100X and 1000X's are entered twice as group members.)

Another strange thing is in the ispconfig control panel if i uncheck the ftp flag for web 1 it is still checked after I click save. I think maybe I should format the box and rebuild it but I can't afford the time. I look forward to reading your advice.

I know your all very busy, so please know I am very grateful for any suggestions you may be able to offer.